The primary data document delivered by IPUMS is a fixed-width text file containing each observation as a single row and each variable as a set of columns. You can use the STATA, SPSS, or SAS (whichever makes the most sense to you) as a guide for column locations and widths and their associated variable names. Using this information with the --cols option in gretl should allow you to read in the data accurately.
Also, I believe gretl is able to read STATA and SPSS files. You can download the extract as an SPSS or STATA data file by changing the the Data Format on the Extract Request page from “Default (fixed-width text)” to your preferred format. One of the options is also a comma delimited format (.csv) which can be read into excel as well as gretl.
If you are at all nervous that the data was not read in correctly, you can check frequencies of individual variables from single samples using the “case-count view” under the codes tab of most variables.
I hope this helps.